Current microarray techniques are subject to inherent variability directly related to the inability of array deposition systems to accurately identify and record the location of arrayed materials and to communicate this information to follow-on systems for use in post-deposition array processing, readout and analysis. The inability to easily identify, record and communicate the accurate location of arrayed materials and any spatial distortions introduced in arrayed materials during post-deposition processing are barriers to automation and integration of array production, processing and analysis. In this SBIR Phase I proposal, Biomachines proposes innovative techniques to incorporate geometric features as "fiducial marks" on microarray and biochip substrates to provide common measurable points for all steps in fabrication, processing and analysis. The use of fiducial marks as fixed reference points will enable a device (e.g., arrayer, imager) to automatically, accurately and repeatedly: align and orient substrates, deposit materials on substrates at pre-determined locations (i.e., "targeting") and identify the location and orientation of materials previously deposited on substrates. BioMachines goal is to automate the entire microarray data extraction process, simplifying analysis software, speeding data production and significantly reducing the variability encountered microarray studies. Under Phase I funding, BioMachines will modify our existing vision guided precision placement platform, including software, to use our proposed fiducial mark technology and will demonstrate the capabilities. BioMachines fiducial mark technology will have broad applications in genomics, proteomics, bioinformatics, biochips, biosensors, cytology and other applications where there is a requirement for repeatedly locating or performing actions on features sized below a few hundred microns.